Variant report

Variant	rs2054257
Chromosome Location	chr8:110332160-110332161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110325503..110327791-chr8:110330957..110333758,2	K562	blood:
2	chr8:110331957..110333774-chr8:110341680..110343638,2	K562	blood:
3	chr8:110332010..110333583-chr8:110343833..110346768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120526	Chromatin interaction
ENSG00000120533	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10087444	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10108349	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1458923	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1531298	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1947629	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1993594	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2125511	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2125513	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2168964	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926195	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926196	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926197	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926208	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926214	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926244	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2926259	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926263	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926265	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926269	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926277	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980589	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2980591	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2980602	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2980606	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2980611	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980619	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980620	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980621	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980623	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980627	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980628	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980630	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980632	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980636	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980637	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3116095	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4734206	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4735117	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4735119	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56247307	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6469248	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6469249	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7003376	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7003806	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7009169	0.82[ASN][1000 genomes]
rs7012304	0.82[ASN][1000 genomes]
rs7819201	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7839867	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2054257	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110236600-110344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:110284400-110344400	Weak transcription	Fetal Lung	lung
3	chr8:110288600-110344200	Weak transcription	Ovary	ovary
4	chr8:110292000-110333200	Weak transcription	HepG2	liver
5	chr8:110293000-110343600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:110307600-110333000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:110312000-110344000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr8:110312200-110342800	Weak transcription	Left Ventricle	heart
9	chr8:110312400-110344200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr8:110318400-110344000	Weak transcription	NHLF	lung
11	chr8:110318600-110332800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr8:110318600-110342800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:110318800-110335200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr8:110319400-110344200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr8:110322000-110344200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:110323200-110335400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr8:110323200-110340000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:110323600-110332400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:110323600-110333000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr8:110323600-110335400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:110324000-110335600	Weak transcription	Thymus	Thymus
22	chr8:110324000-110345400	Weak transcription	Aorta	Aorta
23	chr8:110324200-110340400	Weak transcription	K562	blood
24	chr8:110324800-110344000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:110325200-110333000	Weak transcription	Dnd41	blood
26	chr8:110325200-110341400	Weak transcription	HSMM	muscle
27	chr8:110325200-110342000	Weak transcription	A549	lung
28	chr8:110325200-110344400	Weak transcription	Pancreas	Pancrea
29	chr8:110325200-110344400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr8:110325200-110344400	Weak transcription	Small Intestine	intestine
31	chr8:110325200-110344800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr8:110325400-110337400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr8:110325400-110344200	Weak transcription	Fetal Heart	heart
34	chr8:110325800-110337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:110326600-110335200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:110326600-110344000	Weak transcription	Osteobl	bone
37	chr8:110327800-110338600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr8:110328000-110344400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:110328200-110333000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:110328200-110333400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr8:110328200-110337800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:110328200-110339600	Weak transcription	HUVEC	blood vessel
43	chr8:110328200-110344200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr8:110328200-110345000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr8:110328800-110333000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr8:110328800-110344200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:110329000-110343600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr8:110329400-110344200	Weak transcription	NHEK	skin
49	chr8:110329600-110332600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr8:110329800-110334800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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